SMTL ID : 6hgq.1 (1 other biounit)

Crystal Structure of Human APRT wild type in complex with Hypoxanthine, PRPP and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: V.23, V.24, R.26, E.103, L.158, S.160, E.179 Ligands: HPA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.24, A:V.24, A:R.26, A:E.179

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.64, S.65 Ligands: PRP.3 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: D.64, S.65 Ligands: PRP.6 No protein-ligand interaction detected (PLIP)

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.3: 19 residues within 4Å: Chain A: D.64, S.65, R.66, K.87, L.102, E.103, Y.104, D.126, D.127, L.128, L.129, A.130, T.131, G.132, G.133, T.134 Chain B: R.86 Ligands: MG.2, HPA.4 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.65, A:R.66, A:R.66, A:E.103, A:Y.104, A:Y.104, A:D.126, A:A.130, A:T.131, A:G.132, A:G.133, A:T.134, A:T.134 Water bridges: A:G.67, A:K.87, A:K.87, A:Y.104, A:Y.104, A:M.135 Salt bridges: A:R.66, A:R.66, A:R.66, A:K.87, A:K.87, B:R.86, B:K.90 PRP.6: 20 residues within 4Å: Chain A: R.86, K.90 Chain B: D.64, S.65, R.66, K.87, L.102, E.103, Y.104, D.126, D.127, L.128, L.129, A.130, T.131, G.132, G.133, T.134 Ligands: MG.5, HPA.7 25 PLIP interactions: 22 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.65, B:R.66, B:R.66, B:E.103, B:Y.104, B:D.126, B:A.130, B:T.131, B:G.132, B:G.133, B:T.134, B:T.134 Water bridges: B:K.87, B:K.87, B:K.87, B:K.87, B:M.135 Salt bridges: B:R.66, B:R.66, B:R.66, B:K.87, B:K.87, A:R.86, A:K.90, A:K.90

2 x HPA: HYPOXANTHINE(Non-covalent)

HPA.4: 12 residues within 4Å: Chain A: V.23, V.24, F.25, R.26, R.66, E.103, Y.104, L.128, A.130, L.158 Ligands: GOL.1, PRP.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.24, A:R.26, A:R.66, A:R.66, A:E.103, A:E.103 HPA.7: 11 residues within 4Å: Chain B: V.23, V.24, F.25, R.26, R.66, E.103, Y.104, L.128, A.130, L.158 Ligands: PRP.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:V.24, B:R.26, B:R.66, B:R.66, B:E.103, B:E.103 Water bridges: B:V.24 pi-Stacking: B:F.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozeir, M. et al., Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction. J.Biol.Chem. (2019)

Release Date

2019-07-31

Peptides

Adenine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenine phosphoribosyltransferase

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